InhaltsangabeComparative Genomics-Volume II Table of Contents Section VComparative Analysis of Domain and Protein Families 1. Computational Prediction of Domain Interactions Philipp Pagel, Normann Strack, Matthias Oesterheld, Volker Stümpflen, and Dmitrij Frishman 2. DomainTeam: Synteny of domains is a new approach in comparative genomics Sophie Pasek 3. Inference of gene function based on gene fusion events: the Rosetta Stone method Karsten Suhre 4. Pfam: A domain-centric method for analyzing proteins and proteomes Jaina Mistry and Robert Finn 5. InterPro and InterProScan-Tools for Protein Sequence Classification and Comparison Nicola Mulder and Rolf Apweiler 6. Gene Annotation and Pathway Mapping in KEGG Kiyoko F. Aoki-Kinoshita and Minoru Kanehisa Section VIOrthologs, Synteny, and Genome Evolution 7. Ortholog Detection using the Smallest Distance Algorithm Dennis P. Wall and Todd DeLuca 8. Finding Conserved Gene Order Across Multiple Genomes Giulio Pavesi and Graziano Pesole 9. Analysis of Genome Rearrangement by Block-Interchanges Chin Lung Lu, Ying Chih Lin, Yen Lin Huang, and Chuan Yi Tang 10. Analyzing Patterns of microbial evolution using the Mauve Genome Alignment System Aaron E. Darling, Todd J. Treangen, Xavier Messeguer, and Nicole T. Perna 11. Visualization of syntenic relationships with SynBrowse Volker Brendel, Stefan Kurtz, and Xiaohang Pan 12. GECKO and GHOSTFAM: Rigorous and Efficient Gene Cluster Detection in Prokaryotic Genomes Thomas Schmidt and Jens Stoye Section VIIExperimental Analysis of Whole GenomesAnalysis of Copy Number and Sequence Polymorphisms 13. Genomewide copy number analysis on GeneChip platform using CNAG 2.0 software Seishi Ogawa, Yasuhito Nanya, and Go Yamamoto 14. Oligonucleotide array comparative genomic hybridization Paul van den IJssel and Bauke Ylstra 15. StudyingBacterial Genome Dynamics Using Microarray-Based Comparative Genomic Hybridization Eduardo N. Taboada, Christian C. Luebbert, and John H.E. Nash 16. CGH analysis using the CGHAnalyzer Joel Greshock 17. Microarray-based Approach for Genome-Wide Survey of Nucleotide Polymorphisms Brian W. Brunelle and Tracy L. Nicholson 18. HighThroughput Genotyping of Single Nucleotide Polymorphisms with High Sensitivity Honghua Li, Hui-Yun Wang, Xiangfeng Cui, Minjie Luo, Guohong Hu, Danielle M. Greenawalt, Irina V. Tereshchenko, James Y. Li, Yi Chu, and Richeng Gao 19. Single nucleotide polymorphism (SNP) mapping array assay Xiaofeng Zhou and David T. W. Wong 20. Molecular Inversion Probe Assays Farnaz Absalan and Mostafa Ronaghi 21. novoSNP: variant detection and sequence annotation in resequencing projects Peter De Rijk and Jurgen Del-Favero 22. Rapid Identification of Single Nucleotide Substitutions Using SeqDoc Mark L. Crowe 23. SNPHunter: A Versatile Web-Based Tool for Acquiring and Managing Single Nucleotide Polymorphisms Tianhua Niu 24. Identification of Disease Genes: An Example-driven Web-based Tutorial Medha Bhagwat 25. Variable number tandem repeat typing of bacteria Siamak P. Yazdankhah and Bjørn-Arne Lindstedt 26. Fluorescent amplified fragment length polymorphism (FAFLP) genotyping of bacterial species Meeta Desai 27. FLPmapping: A universal, costeffective, and automatable method for gene mapping Knud Nairz, Peder Zipperlen, and Manuel Schneider

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Comparative Genomics-Volume II Table of Contents Section V-Comparative Analysis of Domain and Protein Families 1. Computational Prediction of Domain Interactions Philipp Pagel, Normann Strack, Matthias Oesterheld, Volker Stümpflen, and Dmitrij Frishman 2. DomainTeam: Synteny of domains is a new approach in comparative genomics Sophie Pasek 3. Inference of gene function based on gene fusion events: the Rosetta Stone method Karsten Suhre 4. Pfam: A domain-centric method for analyzing proteins and proteomes Jaina Mistry and Robert Finn 5. InterPro and InterProScan-Tools for Protein Sequence Classification and Comparison Nicola Mulder and Rolf Apweiler 6. Gene Annotation and Pathway Mapping in KEGG Kiyoko F. Aoki-Kinoshita and Minoru Kanehisa Section VI-Orthologs, Synteny, and Genome Evolution 7. Ortholog Detection using the Smallest Distance Algorithm Dennis P. Wall and Todd DeLuca 8. Finding Conserved Gene Order Across Multiple Genomes Giulio Pavesi and Graziano Pesole 9. Analysis of Genome Rearrangement by Block-Interchanges Chin Lung Lu, Ying Chih Lin, Yen Lin Huang, and Chuan Yi Tang 10. Analyzing Patterns of microbial evolution using the Mauve Genome Alignment System Aaron E. Darling, Todd J. Treangen, Xavier Messeguer, and Nicole T. Perna 11. Visualization of syntenic relationships with SynBrowse Volker Brendel, Stefan Kurtz, and Xiaohang Pan 12. GECKO and GHOSTFAM: Rigorous and Efficient Gene Cluster Detection in Prokaryotic Genomes Thomas Schmidt and Jens Stoye Section VII-Experimental Analysis of Whole Genomes-Analysis of Copy Number and Sequence Polymorphisms 13. Genome-wide copy number analysis on GeneChip platform using CNAG 2.0 software Seishi Ogawa, Yasuhito Nanya, and Go Yamamoto 14. Oligonucleotide array comparative genomic hybridization Paul van den IJssel and Bauke Ylstra 15. Studying Bacterial Genome Dynamics Using Microarray-Based Comparative Genomic Hybridization Eduardo N. Taboada, Christian C. Luebbert, and John H.E. Nash 16. CGH analysis using the CGHAnalyzer Joel Greshock 17. Microarray-based Approach for Genome-Wide Survey of Nucleotide Polymorphisms Brian W. Brunelle and Tracy L. Nicholson 18. High-Throughput Genotyping of Single Nucleotide Polymorphisms with High Sensitivity Honghua Li, Hui-Yun Wang, Xiangfeng Cui, Minjie Luo, Guohong Hu, Danielle M. Greenawalt, Irina V. Tereshchenko, James Y. Li, Yi Chu, and Richeng Gao 19. Single nucleotide polymorphism (SNP) mapping array assay Xiaofeng Zhou and David T. W. Wong 20. Molecular Inversion Probe Assays Farnaz Absalan and Mostafa Ronaghi 21. novoSNP: variant detection and sequence annotation in resequencing projects Peter De Rijk and Jurgen Del-Favero 22. Rapid Identification of Single Nucleotide Substitutions Using SeqDoc Mark L. Crowe 23. SNPHunter: A Versatile Web-Based Tool for Acquiring and Managing Single Nucleotide Polymorphisms Tianhua Niu 24. Identification of Disease Genes: An Example-driven Web-based Tutorial Medha Bhagwat 25. Variable number tandem repeat typing of bacteria Siamak P. Yazdankhah and Bjorn-Arne Lindstedt 26. Fluorescent amplified fragment length polymorphism (FAFLP) genotyping of bacterial species Meeta Desai 27. FLP-mapping: A universal, cost-effective, and automatable method for gene mapping Knud Nairz, Peder Zipperlen, and Manuel Schneider